The great potential of prebiotics and probiotics for the improvement of public health remains largely unrealized. This one-day conference, Probiotics, Prebiotics, and the Host Microbiome: The Science of Translation, jointly presented by the International Scientific Association for Probiotics and Prebiotics and The Sackler Institute for Nutrition Science at the New York Academy of Sciences on June 12, 2013, will explore and have important, broad impact on our understanding of the strong convergence of prebiotic and probiotic biology and its role within the human microbiome framework, thereby informing development of future strategies to translate this knowledge into innovative, economical, and population-wide nutritional and biotherapeutic applications of significant public health benefit. Anticipated to convene 200 attendees across a wide range of scientific and clinical disciplines, bacterial species, and regulatory/policy arenas, the meeting will: (i) Provide a neutral forum, through lectures, interactive panels, and networking activities, for discussing current and emerging concepts of prebiotic and probiotic biology, including the effect on the human microbiome - fostering the development of preventative and biotherapeutic strategies to manipulate the microbiome through functional foods; (ii) Showcase early career, female and underrepresented minority investigators via short talks, posters, awards, travel fellowships, and discounted registration; and (iii) Foster collaboration among junior and senior representatives from academia, clinical care, government and regulatory agencies, and the nutrition industry, to promote knowledge exchange leading to successful translation of research into improved interventions, therapies, and policy with regard to functional foods. The conference is especially timely given the increase in robust scientific evidence supporting the beneficial health effects of prebiotics and probiotics, providing great future potential to build on this knowledge. Examining this evidence in order to inform decision making by the public, health care professionals, and policymakers about the integration of prebiotics and probiotics as functional foods and biotherapeutics is particularly urgent in light of the clinical and economic challenges faced by global health care systems, such as the obesity epidemic and malnutrition. Thematically, the conference goals align well with the mission of NCCAM to define, through rigorous scientific investigation, the usefulness and safety of complementary and alternative medicine interventions and their roles in improving health and health care. The inclusion of data relating to obesity, diabetes, and disorders of the gastrointestinal system also aligns well with the mission of the NIDDK. Publication of an enduring, open-access Meeting Report in Annals of the New York Academy of Sciences will inform science policy and ultimately foster the integration of prebiotics and probiotics in health care recommendations for the prevention and treatment of a multitude of human diseases.